| Variant ID: vg0905315058 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5315058 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )
GCCGAAGCTGAAGTCGGTGCTAACCAGGAGCCCCCGACTGGAAACCAGTCGGATGCAGGGCCAAGCCAAAAGATTCCCGAGATTGAAGCTCAAACGAACA[G/A]
TCCTCTCGGGAAGGATGCTGACAATTAATCAGAAACCAGATCTCCTGTGAAGGCACCAAAGTCCACTCGTCCCCGACCGGGAATCATCACAGGTAGACAT
ATGTCTACCTGTGATGATTCCCGGTCGGGGACGAGTGGACTTTGGTGCCTTCACAGGAGATCTGGTTTCTGATTAATTGTCAGCATCCTTCCCGAGAGGA[C/T]
TGTTCGTTTGAGCTTCAATCTCGGGAATCTTTTGGCTTGGCCCTGCATCCGACTGGTTTCCAGTCGGGGGCTCCTGGTTAGCACCGACTTCAGCTTCGGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.00% | 14.00% | 13.94% | 0.00% | NA |
| All Indica | 2759 | 53.20% | 23.90% | 22.87% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.46% | 0.00% | NA |
| Aus | 269 | 96.70% | 0.00% | 3.35% | 0.00% | NA |
| Indica I | 595 | 43.50% | 22.90% | 33.61% | 0.00% | NA |
| Indica II | 465 | 64.30% | 12.50% | 23.23% | 0.00% | NA |
| Indica III | 913 | 53.00% | 32.20% | 14.79% | 0.00% | NA |
| Indica Intermediate | 786 | 54.30% | 21.80% | 23.92% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 12.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905315058 | G -> A | LOC_Os09g09800.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:15.684; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905315058 | NA | 7.34E-06 | mr1846 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0905315058 | NA | 6.07E-10 | mr1830_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0905315058 | 3.26E-06 | NA | mr1846_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0905315058 | 1.39E-06 | 4.62E-17 | mr1846_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |